Using the FI2000

Hey everyone, I have a 2005 hayabusa and the only additions I have done to the bike are:

new sprokets
Air Box Mode
K&N filter

I put shorty pipes with baffles and now I tkk them off and put back the original yoshi slip ons I had, and I am trying to install the FI2000. I used the settings that were given on the instructions, set for slip ons and the bikes runs like crap. Am I doing anything wrong? I went riding yesterday and she sputter after we rode for maybe 1/2 an HR. She also shut off a few times, maybe running too rich, anyone now what the settings should be?

Thanks "New Guy"

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